Open Source Java Bio-Informatics Software - Page 8

A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).

Error-corrector for pyrosequenced amplicon reads.

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.

Adamant is a java application for annotation of microarray array designs. The software enables MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repos

AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in biology. Examples include the distinguishing of leaf shapes, fish sex, organ size and so forth. AgED is intended for scientific use only. Use and distribution of this technology is subject to the Java Research License included herein. AgED comes with absolutely no warranty.

Agent-based multiscale model of cancer proliferation dynamics

AgentCell is an agent-based model of cellular biochemical processes and biological behavior.

Discovery Manager for integrating components on CSF.

Projet de 2e année d'ingé

Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them

Anatrolivre é um programa para análise de troncos.

Help us to improve Lab Processes. We want to hear your feedback! Request new Lab Processes feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/lp The Animal Studies module is a comprehensive and straightforward application specially designed for biologists and chemists who need to conduct a wide variety of tests and experiments on animals. Animal Studies requires minimal computing skills. Genetic and physiological data can be entered either manually or automatically when automated genotyping and analytical phenotypic assays are used. Animal Studies application is web-based and completely customizable, with Animal Studies it is very simple to create, change and distribute data flows using an iterative approach. Animal Studies puts all the information right at your fingertips. If you are experiencing problems using the Animal Studies System then please report your problem to support@atgclabs.com

Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.

Annotare is a tool for annotating Microarray and Gene Expression data. It will help a bench biologist construct a MIAME-compliant MAGE-TAB file.

Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.

This program serves to provide any useful information regarding a set of loci on the genome. For every genomic position provided, the Annotater will return any "known" information regarding that position.

A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc

The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.

Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina call files) * work with genetic maps ...

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas

A phologenetic supertree construction/assembly tool using triplet similarity as the objective function.

AutoMATRIX is a tool to predict key transcription factors in microarray experiments.